[gmx-users] How to specify .mdp file for position restrained simulation?

[Yang Ye]

A side note to -DPOSRES, it is actually a C preprocessor defined 
variable. There is a corresponding

#ifdef POSRES
...
#endif

in the topology file you built. It is default to POSRES, but you can 
rename it to other name and change accordingly the "define=.." line in 
the mdp file. Also, you can use this mechanism to do position restraint 
MD with different parts of the system, or gradually give freedom to the 
system.

Regards,
Yang Ye

On 11/20/2007 4:18 PM, Maik Goette wrote:
> Hi
>
> Use the following term in your mdp:
> define                   = -DPOSRES
>
> Now, everything is true, depending on the question you ask and the 
> point you're standing...
>
> What you may mean is the following:
> POSRES-Sims are mostly (not always) used for equilibrating the solvent 
> around the protein. These simulations are in general quite short, 
> because relaxation of water happens quite fast.
> In this case a Posres-Sim is much shorter (say 200ps or so) than a 
> "real" run (usually in the range of ns).
> Please be aware, that there is also a parameter file for 
> position-restraints (e.g. posre.itp), which, if automatically 
> generated by pdb2gmx contains the positions of all heavy atoms with a 
> force constant for x,y,z.
>
> And now a suggestion. Please, before starting MD inform yourself about:
> a. The theoretical aspects of molecular dynamics
> b. The program you are using (i.e. the manual)
>
> The probability of getting good results and no crap increases 
> dramatically with following the two points above...
>
> Regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>         mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> Peggy Yao wrote:
>> Hi,
>>
>> How to specify the .mdp file in order to run position restrained
>> simulation? From the examples I found on the internet, it seems that
>> the only difference between the .mdp file for position restrained
>> simulation and the one for actual MD simulation is the simulation time
>> -- the position restrained simulation is much shorter. Is this
>> observation true in general?
>>
>> If yes, usually, how long is enough for the position restrained 
>> simulation?
>>
>> If not, how to specify the .mdp file for position restrained 
>> simulation then?
>>
>> Thanks a lot!
>>
>> Peggy
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